50 research outputs found
The project MinE databrowser: bringing large-scale whole-genome sequencing in ALS to researchers and the public
No full textAmyotrophic lateral sclerosis (ALS) is a rapidly progressive fatal neurodegenerative disease affecting one in 350 people. The aim of Project MinE is to elucidate the pathophysiology of ALS through whole-genome sequencing at least 15,000 ALS patients and 7500 controls at 30× coverage. Here, we present the Project MinE data browser ( databrowser.projectmine.com ), a unique and intuitive one-stop, open-access server that provides detailed information on genetic variation analyzed in a new and still growing set of 4366 ALS cases and 1832 matched controls. Through its visual components and interactive design, the browser specifically aims to be a resource to those without a biostatistics background and allow clinicians and preclinical researchers to integrate Project MinE data into their own research. The browser allows users to query a transcript and immediately access a unique combination of detailed (meta)data, annotations and association statistics that would otherwise require analytic expertise and visits to scattered resources
The Effect of SMN Gene Dosage on ALS Risk and Disease Severity
No full textOBJECTIVE: The role of the survival of motor neuron (SMN) gene in amyotrophic lateral sclerosis (ALS) is unclear, with several conflicting reports. A decisive result on this topic is needed, given that treatment options are available now for SMN deficiency. METHODS: In this largest multicenter case control study to evaluate the effect of SMN1 and SMN2 copy numbers in ALS, we used whole genome sequencing data from Project MinE data freeze 2. SMN copy numbers of 6,375 patients with ALS and 2,412 controls were called from whole genome sequencing data, and the reliability of the calls was tested with multiplex ligation-dependent probe amplification data. RESULTS: The copy number distribution of SMN1 and SMN2 between cases and controls did not show any statistical differences (binomial multivariate logistic regression SMN1 p = 0.54 and SMN2 p = 0.49). In addition, the copy number of SMN did not associate with patient survival (Royston-Parmar; SMN1 p = 0.78 and SMN2 p = 0.23) or age at onset (Royston-Parmar; SMN1 p = 0.75 and SMN2 p = 0.63). INTERPRETATION: In our well-powered study, there was no association of SMN1 or SMN2 copy numbers with the risk of ALS or ALS disease severity. This suggests that changing SMN protein levels in the physiological range may not modify ALS disease course. This is an important finding in the light of emerging therapies targeted at SMN deficiencies. ANN NEUROL 2021;89:686-697
Rare Variant Burden Analysis within Enhancers Identifies CAV1 as an ALS Risk Gene
No full textAmyotrophic lateral sclerosis (ALS) is an incurable neurodegenerative disease. CAV1 and CAV2 organize membrane lipid rafts (MLRs) important for cell signaling and neuronal survival, and overexpression of CAV1 ameliorates ALS phenotypes in vivo. Genome-wide association studies localize a large proportion of ALS risk variants within the non-coding genome, but further characterization has been limited by lack of appropriate tools. By designing and applying a pipeline to identify pathogenic genetic variation within enhancer elements responsible for regulating gene expression, we identify disease-associated variation within CAV1/CAV2 enhancers, which replicate in an independent cohort. Discovered enhancer mutations reduce CAV1/CAV2 expression and disrupt MLRs in patient-derived cells, and CRISPR-Cas9 perturbation proximate to a patient mutation is sufficient to reduce CAV1/CAV2 expression in neurons. Additional enrichment of ALS-associated mutations within CAV1 exons positions CAV1 as an ALS risk gene. We propose CAV1/CAV2 overexpression as a personalized medicine target for ALS.sponsorship: This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (no. 772376 -EScORIAL). The project is supported through the following funding organizations under the aegis of JPND: Medical Research Council (MR/L501529/1 and MR/R024804/1) and Economic and Social Research Council (ES/L008238/1). The collaboration project is co-funded by the PPP Allowance made available by Health~Holland, Top Sector Life Sciences & Health to stimulate public-private partnerships. We acknowledge support from a Lee Newton PhD studentship (T.M.), ``My Name''5 Doddie Foundation (J.P.F.), the Wellcome Trust (J.C.-K., 216596/Z/19/Z; D.B., 213501/Z/18/Z), and NIHR (P.J.S. and A.A.C.). This work was also supported by the NIHR Sheffield Biomedical Research Centre for Translational Neuroscience. Biosample collection was supported by the MND Association and the Wellcome Trust (P.J.S.). We are very grateful to those ALS patients and control subjects who generously donated biosamples. (European Research Council (ERC) under the European Union|772376 -EScORIAL, aegis of JPND: Medical Research Council|MR/L501529/1, aegis of JPND: Medical Research Council|MR/R024804/1, Economic and Social Research Council|ES/L008238/1, Lee Newton PhD studentship, Wellcome Trust, NIHR, NIHR Sheffield Biomedical Research Centre for Translational Neuroscience, MND Association, MRC|MR/R024804/1, MRC|G0600974, Academy of Medical Sciences (AMS)|SGL018\\1007, National Institute for Health Research|CL-2015-04-001)status: Publishe
Project MinE: study design and pilot analyses of a large-scale whole-genome sequencing study in amyotrophic lateral sclerosis [preprint]
No full textFull author list omitted for brevity. For the full list of authors, see article.The most recent genome-wide association study in amyotrophic lateral sclerosis (ALS) demonstrates a disproportionate contribution from low-frequency variants to genetic susceptibility of disease. We have therefore begun Project MinE, an international collaboration that seeks to analyse whole-genome sequence data of at least 15,000 ALS patients and 7,500 controls. Here, we report on the design of Project MinE and pilot analyses of newly whole-genome sequenced 1,264 ALS patients and 611 controls drawn from the Netherlands. As has become characteristic of sequencing studies, we find an abundance of rare genetic variation (minor allele frequency < 0.1%), the vast majority of which is absent in public data sets. Principal component analysis reveals local geographical clustering of these variants within The Netherlands. We use the whole-genome sequence data to explore the implications of poor geographical matching of cases and controls in a sequence-based disease study and to investigate how ancestry-matched, externally sequenced controls can induce false positive associations. Also, we have publicly released genome-wide minor allele counts in cases and controls, as well as results from genic burden tests
Erratum: Rare variant burden analysis within enhancers identifies CAV1 as an ALS risk gene (Cell Reports (2020) 33(9), (S2211124720314455), (10.1016/j.celrep.2020.108456))
No full text(Cell Reports 33, 108456-1–108456-8.e1–e5; December 1, 2020) In the originally published version of this article, Eran Elhaik was incorrectly spelled in the author list. The corrected author list appears here and with the article online. The authors regret the error
Systematic rare variant analyses identify RAB32 as a susceptibility gene for familial Parkinson’s disease
No full textDespite substantial progress, causal variants are identified only for a minority of familial Parkinson’s disease (PD) cases, leaving high-risk pathogenic variants unidentified1,2. To identify such variants, we uniformly processed exome sequencing data of 2,184 index familial PD cases and 69,775 controls. Exome-wide analyses converged on RAB32 as a novel PD gene identifying c.213C > G/p.S71R as a high-risk variant presenting in ~0.7% of familial PD cases while observed in only 0.004% of controls (odds ratio of 65.5). This variant was confirmed in all cases via Sanger sequencing and segregated with PD in three families. RAB32 encodes a small GTPase known to interact with LRRK2 (refs. 3,4). Functional analyses showed that RAB32 S71R increases LRRK2 kinase activity, as indicated by increased autophosphorylation of LRRK2 S1292. Here our results implicate mutant RAB32 in a key pathological mechanism in PD—LRRK2 kinase activity5–7—and thus provide novel insights into the mechanistic connections between RAB family biology, LRRK2 and PD risk
Whole-genome sequencing reveals that variants in the Interleukin 18 Receptor Accessory Protein 3'UTR protect against ALS
No full textThe noncoding genome is substantially larger than the protein-coding genome but has been largely unexplored by genetic association studies. Here, we performed region-based rare variant association analysis of >25,000 variants in untranslated regions of 6,139 amyotrophic lateral sclerosis (ALS) whole genomes and the whole genomes of 70,403 non-ALS controls. We identified interleukin-18 receptor accessory protein (IL18RAP) 3' untranslated region (3'UTR) variants as significantly enriched in non-ALS genomes and associated with a fivefold reduced risk of developing ALS, and this was replicated in an independent cohort. These variants in the IL18RAP 3'UTR reduce mRNA stability and the binding of double-stranded RNA (dsRNA)-binding proteins. Finally, the variants of the IL18RAP 3'UTR confer a survival advantage for motor neurons because they dampen neurotoxicity of human induced pluripotent stem cell (iPSC)-derived microglia bearing an ALS-associated expansion in C9orf72, and this depends on NF-κB signaling. This study reveals genetic variants that protect against ALS by reducing neuroinflammation and emphasizes the importance of noncoding genetic association studies
ATXN1 repeat expansions confer risk for amyotrophic lateral sclerosis and contribute to TDP-43 mislocalization
No full textIncreasingly, repeat expansions are being identified as part of the complex genetic architecture of amyotrophic lateral sclerosis. To date, several repeat expansions have been genetically associated with the disease: intronic repeat expansions in C9orf72, polyglutamine expansions in ATXN2 and polyalanine expansions in NIPA1. Together with previously published data, the identification of an amyotrophic lateral sclerosis patient with a family history of spinocerebellar ataxia type 1, caused by polyglutamine expansions in ATXN1, suggested a similar disease association for the repeat expansion in ATXN1. We, therefore, performed a large-scale international study in 11 700 individuals, in which we showed a significant association between intermediate ATXN1 repeat expansions and amyotrophic lateral sclerosis (P = 3.33 × 10-7). Subsequent functional experiments have shown that ATXN1 reduces the nucleocytoplasmic ratio of TDP-43 and enhances amyotrophic lateral sclerosis phenotypes in Drosophila, further emphasizing the role of polyglutamine repeat expansions in the pathophysiology of amyotrophic lateral sclerosis
Genome-wide identification of the genetic basis of amyotrophic lateral sclerosis
No full textAmyotrophic lateral sclerosis (ALS) is a complex disease that leads to motor neuron death. Despite heritability estimates of 52%, genome-wide association studies (GWASs) have discovered relatively few loci. We developed a machine learning approach called RefMap, which integrates functional genomics with GWAS summary statistics for gene discovery. With transcriptomic and epigenetic profiling of motor neurons derived from induced pluripotent stem cells (iPSCs), RefMap identified 690 ALS-associated genes that represent a 5-fold increase in recovered heritability. Extensive conservation, transcriptome, network, and rare variant analyses demonstrated the functional significance of candidate genes in healthy and diseased motor neurons and brain tissues. Genetic convergence between common and rare variation highlighted KANK1 as a new ALS gene. Reproducing KANK1 patient mutations in human neurons led to neurotoxicity and demonstrated that TDP-43 mislocalization, a hallmark pathology of ALS, is downstream of axonal dysfunction. RefMap can be readily applied to other complex diseases
Value of systematic genetic screening of patients with amyotrophic lateral sclerosis
No full textThe clinical utility of routine genetic sequencing in amyotrophic lateral sclerosis is uncertain. Our
aim was to determine whether routine targeted sequencing of 44 ALS-relevant genes would have a
significant impact on clinical care and disease subclassification. We performed targeted
sequencing of a 44 gene panel in a prospective case series of 100 consecutive ALS patients
recruited sequentially from the Sheffield Motor Neuron Disorders Clinic, United Kingdom. All
participants were diagnosed with ALS by a specialist Consultant Neurologist. 7/100 patients had
familial ALS, but the majority were apparently sporadic cases.
21% of ALS patients carried a confirmed pathogenic or likely-pathogenic mutation, of whom 93%
had no family history of ALS. 15% met the inclusion criteria for a current ALS genetic-therapy trial.
5/21 patients with a pathogenic mutation had an additional variant of uncertain significance (VUS).
An additional 21% of ALS patients carried a VUS in an ALS-associated gene. Overall, 13% of
patients carried more than one genetic variant (pathogenic or VUS). ALS patients carrying two
variants developed disease at a significantly earlier age compared to patients with a single variant
(median age of onset = 56 versus 60 years, p=0.0074).
In conclusion, routine screening for ALS-associated pathogenic mutations in a specialised ALS
referral clinic will impact clinical care in 21% of cases. An additional 21% of patients have variants
in the ALS gene panel currently of unconfirmed significance after removing non-specific or
predicted benign variants. Overall, variants within known ALS-linked genes are of potential clinical
importance in 42% of patients
